Managing Data

add_bam

add_bam(path: str) -> 'Gw'

Add a BAM file to the visualisation.

Parameters:

  • path (str): Path to the BAM file

Returns:

  • Gw: Self for method chaining

Example:

gw.add_bam("sample.bam")

remove_bam

remove_bam(index: int) -> 'Gw'

Remove a BAM file from the visualisation.

Parameters:

  • index (int): Index of the BAM file to remove

Returns:

  • Gw: Self for method chaining

add_pysam_alignments

add_pysam_alignments(self, pysam_alignments: List['AlignedSegment'], region_index: int = -1, bam_index: int = -1) -> 'Gw'

Add a list of pysam alignments to Gw. Before using this function, you must add a at least one region to Gw using add_region function, and a bam/cram file using add_bam.

Internally, the bam1_t data pointer is passed straight to Gw, so no copies are made during drawing. However, this means input pysam_alignments must ‘outlive’ any drawing calls made by Gw.

If using multiple regions or bams, use the region_index and bam_index arguments to indicate which panel to use for drawing the pysam alignment.

Note, this function assumes alignments are in position sorted order. Also, pysam alignments can not be mixed with ‘normal’ Gw alignment tracks.

Parameters:

  • pysam_alignments List[‘AlignedSegment’]: List of alignments
  • region_index (int): Region index to draw to (the column on the canvas)
  • bam_index (int): Bam index to draw to (the row on the canvas)

Returns:

  • Gw: Self for method chaining

Raises:

  • IndexError: If the region_index or bam_index are out of range
  • RuntimeError: If any normal collections are already present in the Gw object

Example:

import pysam
from gwplot import Gw

# Open alignment file
bam = pysam.AlignmentFile("sample.bam")

# Define region of interest
region = ("chr1", 1000000, 1050000)

# Filter alignments based on custom criteria
filtered_reads = []
for read in bam.fetch(*region):
    # Only keep high-quality reads with specific characteristics
    if read.mapping_quality > 30 and not read.is_duplicate and not read.is_secondary:
        filtered_reads.append(read)

# Visualize only the filtered reads
gw = Gw("hg38")
gw.add_bam("sample.bam")  # Reference to original BAM still needed
gw.add_region(*region)
gw.add_pysam_alignments(filtered_reads)
gw.show()

add_track

add_track(path: str, vcf_as_track: bool = True, bed_as_track: bool = True) -> 'Gw'

Add a genomic data track to the visualisation.

Parameters:

  • path (str): Path to the track file (VCF, BED, etc.)
  • vcf_as_track (bool, optional): Whether to display VCF files as tracks
  • bed_as_track (bool, optional): Whether to display BED files as tracks

Returns:

  • Gw: Self for method chaining

Example:

# Add a VCF file as a track
gw.add_track("variants.vcf")

# Add a BED file
gw.add_track("features.bed")

remove_track

remove_track(index: int) -> 'Gw'

Remove a data track from the visualisation.

Parameters:

  • index (int): Index of the track to remove

Returns:

  • Gw: Self for method chaining

clear

clear() -> None

Remove all data.

clear_alignments

clear_alignments() -> None

Remove all loaded alignment data.

clear_regions

clear_regions() -> None

Remove all defined genomic regions.